I'm trying to use the CTMU on a PIC24F16KA302 to measure the time difference between two pulses and I can't get the second edge to register.
I have it setup so that the first edge triggers on the edge of CTED1 (pin 20 of the 28 pin pic) and the second edge should trigger on the rising edge of CTED2 (pin 23). I can see that the edges on my oscilloscope and everything is fine there, but the PIC never detects edge 2. Any suggestions?

Have you checked the analog configuration bits for any pins you want for digital input that have analog functions? I think the default is to disable the digital input buffer. Check the ANSA, ANSB, ANSC registers for proper configuration.